Note
Go to the end to download the full example code.
8.7. Run junifer and julearn.¶
This example uses a ParcelAggregation marker to compute the mean of each parcel using the Schaefer parcellation (100 rois, 7 Yeo networks) for a 3D nifti to extract some features for machine learning using julearn to predict some other data.
Authors: Leonard Sasse, Sami Hamdan, Nicolas Nieto, Synchon Mandal
License: BSD 3 clause
import tempfile
import nilearn
import pandas as pd
from julearn import run_cross_validation, PipelineCreator
import junifer.testing.registry # noqa: F401
from junifer.api import collect, run
from junifer.storage.sqlite import SQLiteFeatureStorage
from junifer.utils import configure_logging
Set the logging level to info to see extra information:
configure_logging(level="INFO")
2024-08-14 13:31:37,193 - JUNIFER - INFO - ===== Lib Versions =====
2024-08-14 13:31:37,193 - JUNIFER - INFO - numpy: 1.26.4
2024-08-14 13:31:37,193 - JUNIFER - INFO - scipy: 1.14.0
2024-08-14 13:31:37,193 - JUNIFER - INFO - pandas: 2.1.4
2024-08-14 13:31:37,193 - JUNIFER - INFO - nilearn: 0.10.4
2024-08-14 13:31:37,193 - JUNIFER - INFO - nibabel: 5.2.1
2024-08-14 13:31:37,193 - JUNIFER - INFO - junifer: 0.0.6.dev23
2024-08-14 13:31:37,193 - JUNIFER - INFO - ========================
Define the markers you want:
marker_dicts = [
{
"name": "Schaefer100x17_TrimMean80",
"kind": "ParcelAggregation",
"parcellation": "Schaefer100x17",
"method": "trim_mean",
"method_params": {"proportiontocut": 0.2},
},
{
"name": "Schaefer200x17_Mean",
"kind": "ParcelAggregation",
"parcellation": "Schaefer200x17",
"method": "mean",
},
]
Define target and confounds for julearn machine learning:
Load the VBM phenotype data for machine learning data: - Fetch the Oasis dataset
oasis_dataset = nilearn.datasets.fetch_oasis_vbm()
age = oasis_dataset.ext_vars[y][:10]
sex = (
pd.Series(oasis_dataset.ext_vars["mf"][:10])
.map(lambda x: 1 if x == "F" else 0)
.values
)
Create a temporary directory for junifer feature extraction:
with tempfile.TemporaryDirectory() as tmpdir:
storage = {"kind": "SQLiteFeatureStorage", "uri": f"{tmpdir}/test.sqlite"}
# run the defined junifer feature extraction pipeline
run(
workdir="/tmp",
datagrabber={"kind": "OasisVBMTestingDataGrabber"},
markers=marker_dicts,
storage=storage,
)
# read in extracted features and add confounds and targets
# for julearn run cross validation
collect(storage)
db = SQLiteFeatureStorage(uri=storage["uri"])
df_vbm = db.read_df(feature_name="VBM_GM_Schaefer200x17_Mean_aggregation")
oasis_subjects = [x[0] for x in df_vbm.index]
df_vbm.index = oasis_subjects
2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker Collection
2024-08-14 13:31:37,207 - JUNIFER - INFO - DataGrabber output type: ['VBM_GM']
2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Data Reader:
2024-08-14 13:31:37,207 - JUNIFER - INFO - Data Reader output type: ['VBM_GM']
2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker: Schaefer100x17_TrimMean80
2024-08-14 13:31:37,207 - JUNIFER - INFO - Marker output type: ['vector']
2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating storage for Schaefer100x17_TrimMean80
2024-08-14 13:31:37,207 - JUNIFER - INFO - Validating Marker: Schaefer200x17_Mean
2024-08-14 13:31:37,208 - JUNIFER - INFO - Marker output type: ['vector']
2024-08-14 13:31:37,208 - JUNIFER - INFO - Validating storage for Schaefer200x17_Mean
2024-08-14 13:31:37,212 - JUNIFER - INFO - Getting element sub-01
2024-08-14 13:31:37,212 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:31:37,212 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0001_MR1/mwrc1OAS1_0001_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:31:37,212 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:31:37,213 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:31:37,213 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:37,213 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:37,214 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:37,214 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:37,214 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:31:37,214 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:37,215 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:37,245 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:38,273 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:38,370 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsk_7rlurr/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsk_7rlurr/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpyf0mk8g3/parcellations01lh7bnf/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:39,758 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:31:40,778 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:31:40,811 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:31:40,811 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:40,812 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:40,812 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:40,812 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:40,812 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:31:40,812 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:40,813 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:40,844 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:41,894 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:41,991 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsn1cbu0s3/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsn1cbu0s3/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpyf0mk8g3/parcellations76xt8d63/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:44,030 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:31:45,057 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:31:45,103 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:31:45,104 - JUNIFER - INFO - Getting element sub-02
2024-08-14 13:31:45,104 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:31:45,104 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0002_MR1/mwrc1OAS1_0002_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:31:45,104 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:31:45,105 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:31:45,105 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:45,105 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:45,105 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:45,105 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:45,105 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:31:45,106 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:45,107 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:45,136 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:46,172 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:46,268 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsze7on4ow/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsze7on4ow/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpehxlabxz/parcellationslsci3gpa/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:47,672 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:31:48,693 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:31:48,728 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:31:48,728 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:48,729 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:48,729 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:48,729 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:48,729 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:31:48,729 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:48,730 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:48,761 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:49,798 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:49,895 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations_n837ejg/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations_n837ejg/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpehxlabxz/parcellationsea2v8nng/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:51,924 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:31:52,911 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:31:52,958 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:31:52,959 - JUNIFER - INFO - Getting element sub-03
2024-08-14 13:31:52,959 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:31:52,959 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:31:52,959 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:31:52,960 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:31:52,960 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:52,960 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:52,960 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:52,961 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:52,961 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:31:52,961 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:52,962 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:52,991 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:54,002 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:54,099 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationskhx67939/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationskhx67939/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmplbrzzzt_/parcellationscn0krced/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:55,485 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:31:56,487 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:31:56,518 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:31:56,518 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:31:56,518 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:31:56,519 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:31:56,519 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:31:56,519 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:31:56,519 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:31:56,520 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:31:56,550 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:31:57,578 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:31:57,675 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsp7_2emuc/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsp7_2emuc/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmplbrzzzt_/parcellations2u0_jtr1/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:31:59,706 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:00,771 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:00,818 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:00,818 - JUNIFER - INFO - Getting element sub-04
2024-08-14 13:32:00,819 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:00,819 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0004_MR1/mwrc1OAS1_0004_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:00,819 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:00,820 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:00,820 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:00,820 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:00,820 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:00,820 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:00,820 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:00,821 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:00,822 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:00,852 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:01,909 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:02,006 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationstp4y7ax8/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationstp4y7ax8/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa8btuy0o/parcellations_s2i5892/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:03,400 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:04,506 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:04,539 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:04,539 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:04,540 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:04,540 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:04,540 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:04,540 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:04,540 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:04,541 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:04,572 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:05,634 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:05,731 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsf56ght22/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsf56ght22/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpa8btuy0o/parcellationseukriiwm/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:07,759 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:08,763 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:08,809 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:08,809 - JUNIFER - INFO - Getting element sub-05
2024-08-14 13:32:08,810 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:08,810 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0005_MR1/mwrc1OAS1_0005_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:08,810 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:08,811 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:08,811 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:08,811 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:08,811 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:08,811 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:08,811 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:08,812 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:08,813 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:08,842 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:09,911 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:10,008 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations3aydknh0/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations3aydknh0/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpqtg8ujtl/parcellationsotc7h1wh/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:11,393 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:12,392 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:12,422 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:12,423 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:12,423 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:12,423 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:12,423 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:12,423 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:12,423 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:12,425 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:12,455 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:13,479 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:13,576 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations756e923l/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations756e923l/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpqtg8ujtl/parcellationsp7jnsh3z/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:15,608 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:16,593 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:16,638 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:16,639 - JUNIFER - INFO - Getting element sub-06
2024-08-14 13:32:16,639 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:16,639 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0006_MR1/mwrc1OAS1_0006_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:16,639 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:16,640 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:16,640 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:16,641 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:16,641 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:16,641 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:16,641 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:16,641 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:16,642 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:16,672 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:17,691 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:17,787 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations__0x6lgs/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations__0x6lgs/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpy93ai3yc/parcellationsg0ee7xqy/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:19,179 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:20,177 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:20,210 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:20,210 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:20,210 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:20,210 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:20,210 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:20,211 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:20,211 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:20,212 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:20,242 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:21,271 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:21,369 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationssj1c90m3/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationssj1c90m3/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpy93ai3yc/parcellations3jcgmobs/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:23,407 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:24,402 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:24,449 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:24,449 - JUNIFER - INFO - Getting element sub-07
2024-08-14 13:32:24,449 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:24,449 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0007_MR1/mwrc1OAS1_0007_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:24,449 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:24,450 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:24,450 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:24,451 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:24,451 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:24,451 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:24,451 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:24,451 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:24,452 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:24,482 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:25,519 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:25,616 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations7h6rfx6r/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations7h6rfx6r/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5xe2_a29/parcellations0e2bl88y/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:27,005 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:28,019 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:28,049 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:28,049 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:28,049 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:28,050 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:28,050 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:28,050 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:28,050 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:28,051 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:28,082 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:29,122 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:29,220 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsfngfzmv9/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsfngfzmv9/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp5xe2_a29/parcellationsgmzoforx/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:31,240 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:32,291 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:32,338 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:32,339 - JUNIFER - INFO - Getting element sub-08
2024-08-14 13:32:32,339 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:32,339 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0009_MR1/mwrc1OAS1_0009_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:32,339 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:32,340 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:32,340 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:32,341 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:32,341 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:32,341 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:32,341 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:32,341 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:32,342 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:32,372 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:33,422 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:33,521 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsaw8_w077/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsaw8_w077/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzugufs9u/parcellationst_44g44z/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:34,909 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:35,985 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:36,018 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:36,018 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:36,019 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:36,019 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:36,019 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:36,019 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:36,019 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:36,021 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:36,051 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:37,112 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:37,210 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations18_tv4sz/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations18_tv4sz/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmpzugufs9u/parcellations2dd0_ar6/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:39,254 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:40,326 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:40,373 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:40,373 - JUNIFER - INFO - Getting element sub-09
2024-08-14 13:32:40,373 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:40,374 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0010_MR1/mwrc1OAS1_0010_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:40,374 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:40,375 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:40,375 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:40,375 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:40,375 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:40,375 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:40,375 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:40,375 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:40,377 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:40,406 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:41,454 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:41,552 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsb0n2se5k/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsb0n2se5k/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmphskxfxzs/parcellationscv61ycth/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:42,941 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:44,046 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:44,080 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:44,080 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:44,081 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:44,081 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:44,081 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:44,081 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:44,081 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:44,082 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:44,113 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:45,166 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:45,264 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsodev0ycx/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsodev0ycx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmphskxfxzs/parcellationsonq8_2nd/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:47,289 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:48,369 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:48,420 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:48,420 - JUNIFER - INFO - Getting element sub-10
2024-08-14 13:32:48,421 - JUNIFER - INFO - Fitting pipeline
2024-08-14 13:32:48,421 - JUNIFER - INFO - Reading VBM_GM from /home/runner/nilearn_data/oasis1/OAS1_0011_MR1/mwrc1OAS1_0011_MR1_mpr_anon_fslswapdim_bet.nii.gz
2024-08-14 13:32:48,421 - JUNIFER - INFO - VBM_GM is of type NIFTI
2024-08-14 13:32:48,422 - JUNIFER - INFO - Fitting marker Schaefer100x17_TrimMean80
2024-08-14 13:32:48,422 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:48,422 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:48,422 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:48,422 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:48,422 - JUNIFER - INFO - n_rois: 100
2024-08-14 13:32:48,423 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:48,424 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:48,454 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:49,506 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:49,603 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellationsbw9yjhtk/Schaefer100x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellationsbw9yjhtk/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6kuq71nf/parcellationsmf3ak3f6/Schaefer100x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:50,983 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:52,041 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:52,075 - JUNIFER - INFO - Fitting marker Schaefer200x17_Mean
2024-08-14 13:32:52,075 - JUNIFER - INFO - Computing VBM_GM
2024-08-14 13:32:52,076 - JUNIFER - INFO - Fetching one of Schaefer parcellations.
2024-08-14 13:32:52,076 - JUNIFER - INFO - Parcellation parameters:
2024-08-14 13:32:52,076 - JUNIFER - INFO - resolution: 2.0
2024-08-14 13:32:52,076 - JUNIFER - INFO - n_rois: 200
2024-08-14 13:32:52,076 - JUNIFER - INFO - yeo_networks: 17
2024-08-14 13:32:52,078 - JUNIFER - INFO - Loading parcellation /home/runner/junifer/data/parcellations/schaefer_2018/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii.gz
2024-08-14 13:32:52,108 - JUNIFER - INFO - Found existing xfm file for MNI152NLin6Asym to MNI152Lin at /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5
2024-08-14 13:32:53,166 - JUNIFER - INFO - Downloading template MNI152Lin in resolution 2
2024-08-14 13:32:53,262 - JUNIFER - INFO - antsApplyTransforms command to be executed:
antsApplyTransforms -d 3 -e 3 -n 'GenericLabel[NearestNeighbor]' -i /tmp/tmpp3v3ecmt/parcellations5nwsw_yx/Schaefer200x17.nii.gz -r /tmp/tmpp3v3ecmt/parcellations5nwsw_yx/MNI152Lin_T1w_2.0.nii.gz -t /home/runner/junifer/data/xfms/MNI152NLin6Asym_to_MNI152Lin/MNI152NLin6Asym_to_MNI152Lin_Composite.h5 -o /tmp/tmp6kuq71nf/parcellations16_zsodk/Schaefer200x17_warped_from_MNI152NLin6Asym_to_MNI152Lin.nii.gz
2024-08-14 13:32:55,286 - JUNIFER - INFO - antsApplyTransforms command succeeded with the following output:
2024-08-14 13:32:56,341 - JUNIFER - INFO - Storing in <SQLiteFeatureStorage @ /tmp/tmpqe457sad/test.sqlite (multiple output)>
2024-08-14 13:32:56,388 - JUNIFER - INFO - Marker collection fitting done
2024-08-14 13:32:56,389 - JUNIFER - INFO - Collecting data using SQLiteFeatureStorage
2024-08-14 13:32:56,389 - JUNIFER - INFO - Collecting data from /tmp/tmpqe457sad/*test.sqlite
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2024-08-14 13:32:57,799 - JUNIFER - INFO - Collect done
Using julearn for machine learning: We predict the age given our vbm features and sex as a confound.
X = list(df_vbm.columns)
df_vbm[y] = age
df_vbm[confound] = sex
X_types = {
"features": X,
"confound": confound,
}
creator = PipelineCreator(problem_type="regression", apply_to="features")
creator.add("zscore", apply_to=["features", "confound"])
creator.add("confound_removal", apply_to="features", confounds="confound")
creator.add("ridge")
scores = run_cross_validation(
X=X + [confound],
y=y,
X_types=X_types,
data=df_vbm,
model=creator,
cv=3,
)
print(scores)
fit_time score_time ... fold cv_mdsum
0 0.134054 0.019021 ... 0 509497eb21da473048117e0c6704d3ea
1 0.131629 0.019209 ... 1 509497eb21da473048117e0c6704d3ea
2 0.131074 0.019018 ... 2 509497eb21da473048117e0c6704d3ea
[3 rows x 8 columns]
Interpretation of results: Doing machine learning with only 10 datapoints is not meaningful. This explains the big variation in scores for different cross-validation folds.
Total running time of the script: (1 minutes 21.352 seconds)